The high-resolution in vivo measurement of replication fork velocity and pausing

Abstract

An important step towards understanding the replication process in the context of the cell is the quantitative characterization of replication dynamics, including the rate of replication fork progression (i.e. fork velocity) with genomic and temporal specificity in vivo. In this paper, we develop a novel method, lag-time analysis, for measuring replisome dynamics using next-generation sequencing. We provide the first quantitative locus-specific measurements of fork velocity. The measured velocity is observed to be both locus and time dependent, even in wild-type cells. To benchmark the approach, we analyze replication dynamics in three different species and a collection of mutants which facilitate the quantitative characterization of replication-conflict-induced fork slowdowns as well as a host of other replication dynamics phenomena, including the observation of temporal fork velocity oscillation. With increases in sequencing depth and improvements in sample preparation, the approach has the potential to provide new insights at higher genomic resolution and in a wide-range of biological systems.